In vet school, we were taught that this term refers to postmortem examinations on animals, versus an autopsy, which is an examination of "self". Since you can't do an examination (or anything!) postmortem, a human examining a human cadaver was said to be doing an autopsy. A human doing a examination on an animal cadaver was said to be doing a necropsy.
In checking with several current online dictionary sources1 through dictionary.com, I see that necropsy and autopsy are used interchangeably.
1Necropsy - Dictionary.com references